Mismatch and academic performance at America’s selective colleges and universities

American selective colleges and universities use affirmative action policies to achieve diversity, given blacks and Latinos have somewhat lower SAT scores than their Asian and white peers. Critics of affirmative action argue that this results in lower grades and greater dropout among underrepresented minority groups. Using the Educational Longitudinal Study, a nationally representative longitudinal data set, we examine the relationship between SAT mismatch and college outcomes for students at selective institutions. We find that mismatch is not associated with graduation from a selective institution, but is associated with lower grades. The negative relationship between mismatch and grades holds for all racial-ethnic groups, not just blacks and Latinos, and is less predictive of academic performance than is high school grade point average. Thus, although mismatch may lower performance at selective colleges, it does not appear to prevent students who may have benefitted from affirmative action from obtaining important credentials from America’s elite educational institutions.     

Transient Acceleration of Epidermal Growth Factor Receptor Dynamics Produces Higher-Order Signaling Clusters

Cell signaling depends on spatiotemporally regulated molecular interactions. Although the movements of signaling proteins have been analyzed with various technologies, how spatial dynamics influence the molecular interactions that transduce signals is unclear. Here, we developed a single-molecule method to analyze the spatiotemporal coupling between motility, clustering, and signaling. The analysis was performed with the epidermal growth factor receptor (EGFR), which triggers signaling through its dimerization and phosphorylation after association with EGF. Our results show that the few EGFRs isolated in membrane subdomains were released by an EGF-dependent increase in their diffusion area, facilitating molecular associations and producing immobile clusters. Using a two-color single-molecule analysis, we found that the EGF-induced state transition alters the properties of the immobile clusters, allowing them to interact for extended periods with the cytoplasmic protein, GRB2. Our study reveals a novel correlation between this molecular interaction and its mesoscale dynamics, providing the initial signaling node.     

Identification of Pak1 inhibitors using water thermodynamic analysis

Abstract

p21-activated kinases (Paks) play an integral component in various cellular diverse processes. The full activation of Pak is dependent upon several serine residues present in the N-terminal region, a threonine present at the activation loop, and finally the phosphorylation of these residues ensure the complete activation of Pak1. The present study deals with the identification of novel potent candidates of Pak1 using computational methods as anti-cancer compounds. A diverse energy based pharmacophore (e-pharmacophore) was developed using four co-crystal inhibitors of Pak1 having pharmacophore features of 5 (DRDRR), 6 (DRHADR), and 7 (RRARDRP and DRRDADH) hypotheses. These models were used for rigorous screening against e-molecule database. The obtained hits were filtered using ADME/T and molecular docking to identify the high affinity binders. These hits were subjected to hierarchical clustering using dendritic fingerprint inorder to identify structurally diverse molecules. The diverse hits were scored against generated water maps to obtain WM/MM ΔG binding energy. Furthermore, molecular dynamics simulation and density functional theory calculations were performed on the final hits to understand the stability of the complexes. Five structurally diverse novel Pak1 inhibitors (4835785, 32198676, 32407813, 76038049, and 32945545) were obtained from virtual screening, water thermodynamics and WM/MM ΔG binding energy. All hits revealed similar mode of binding pattern with the hinge region residues replacing the unstable water molecules in the binding site. The obtained novel hits could be used as a platform to design potent drugs that could be experimentally tested against cancer patients having increased Pak1 expression.     

Integrative structure and function of the yeast exocyst complex

Exocyst is an evolutionarily conserved hetero‐octameric tethering complex that plays a variety of roles in membrane trafficking, including exocytosis, endocytosis, autophagy, cell polarization, cytokinesis, pathogen invasion, and metastasis. Exocyst serves as a platform for interactions between the Rab, Rho, and Ral small GTPases, SNARE proteins, and Sec1/Munc18 regulators that coordinate spatial and temporal fidelity of membrane fusion. However, its mechanism is poorly described at the molecular level. Here, we determine the molecular architecture of the yeast exocyst complex by an integrative approach, based on a 3D density map from negative‐stain electron microscopy (EM) at ~16 Å resolution, 434 disuccinimidyl suberate and 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide hydrochloride cross‐links from chemical‐crosslinking mass spectrometry, and partial atomic models of the eight subunits. The integrative structure is validated by a previously determined cryo‐EM structure, cross‐links, and distances from in vivo fluorescence microscopy. Our subunit configuration is consistent with the cryo‐EM structure, except for Sec5. While not observed in the cryo‐EM map, the integrative model localizes the N‐terminal half of Sec3 near the Sec6 subunit. Limited proteolysis experiments suggest that the conformation of Exo70 is dynamic, which may have functional implications for SNARE and membrane interactions. This study illustrates how integrative modeling based on varied low‐resolution structural data can inform biologically relevant hypotheses, even in the absence of high‐resolution data.     

Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis

Gastric cancer is one of the most common and lethal cancers worldwide. However, despite its clinical importance, the regulatory mechanisms involved in the aggressiveness of this cancer are still poorly understood. A better understanding of the biology, genetics and molecular mechanisms of gastric cancer would be useful in developing novel targeted approaches for treating this disease. In this study we used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in gastric cancer. A primary immunodeficiency pathway, focal adhesion, ECM-receptor interactions and the metabolism of xenobiotics by cytochrome P450 were identified as four important pathways associated with the progression of gastric cancer. The genes in these pathways, e.g., ZAP70, IGLL1, CD79A, COL6A3, COL3A1, COL1A1, CYP2C18 and CYP2C9, may be considered as potential therapeutic targets for gastric cancer.     

Combining affinity enrichment,cross‐linking with photo amino acids,and mass spectrometry for probing protein kinase D2 interactions

We present a novel approach that relies on the affinity capture of protein interaction partners from a complex mixture, followed by their covalent fixation via UV‐induced activation of incorporated diazirine photoreactive amino acids (photo‐methionine and photo‐leucine). The captured protein complexes are enzymatically digested and interacting proteins are identified and quantified by label‐free LC/MS analysis. Using HeLa cell lysates with photo‐methionine and photo‐leucine‐labeled proteins, we were able to capture and preserve protein interactions that are otherwise elusive in conventional pull‐down experiments. Our approach is exemplified for mapping the protein interaction network of protein kinase D2, but has the potential to be applied to any protein system. Data are available via ProteomeXchange with identifiers PXD005346 (photo amino acid incorporation) and PXD005349 (enrichment experiments).     

Genetic diversity of Syrian Arabian horses

Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (H_o) ranged between 0.30 and 0.32, expected heterozygosity (H_e) between 0.30 and 0.31 and inbreeding coefficients (F_is) between ?0.02 and ?0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (F_st < 0.05). Hierarchical clustering showed a clear distinction between Arabian and Przewalski's horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub‐clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity.     

Relationships of growth,stable carbon isotope composition and anatomical properties of leaf and xylem in seven mulberry cultivars: a hint towards drought tolerance

• The fast growth of mulberry depends on high water consumption, but considerable variations in drought tolerance exist across different cultivars. Physiological and anatomical mechanisms are important to plant survival under drought. However, few research efforts have been made to reveal the relationships of these two aspects in relation to drought tolerance.
• In this study, growth rates, leaf functional physiology and anatomical characteristics of leaf and xylem of 1‐year‐old saplings of seven mulberry cultivars at a common garden were compared. Their relationships were also explored.
• Growth, leaf physiology and anatomy were significantly different among the tested cultivars. Foliar stable carbon isotope composition (δ¹³C) was negatively correlated with growth rates, and closely related to several leaf and xylem anatomical traits. Particularly, leaf thickness, predicted hydraulic conductivity and vessel element length jointly contributed 77% of the variability in δ¹³C. Cultivar Wupu had small stomata, intermediate leaf thickness, the smallest hydraulically weighted vessel diameter and highest vessel number, and higher δ¹³C; Yunguo1 had high abaxial stomatal density, low specific leaf area, moderate hydraulic conductivity and δ¹³C; these are beneficial features to reduce leaf water loss and drought‐induced xylem embolism in arid areas. Cultivar Liaolu11 had contrasting physiological and anatomical traits compared with the previous two cultivars, suggesting that it might be sensitive to drought.
• Our findings indicate that growth and δ¹³C are closely associated with both leaf and xylem anatomical characteristics in mulberry, which provides fundamental information to assist evaluation of drought tolerance in mulberry cultivars and in other woody trees.

     

神农架川金丝猴栖息地森林群落的数量分类与排序

在神农架川金丝猴生境典型地段设立样方58块,根据样方资料对神农架川金丝猴栖息地的森林群落用组平均法分类和DCA排序.用组平均法将58块样地分为9个群系,依据《中国植被》的分类原则和系统将研究区植物群落划归为7个植被型.样地的DCA排序较好地揭示了该区森林群落的分布格局与环境梯度的关系;DCA第二轴明显地反映出森林群落的海拔梯度变化,沿DCA第二轴从右到左,海拔逐渐升高;第一轴表现了各植物群落或植物种所在环境的坡度、坡向,即水分和光照因素,沿第一轴从下到上,坡度渐缓、坡向渐向阳.其中海拔梯度是环境因子中对森林群落起决定性作用的因子.研究表明,巴山冷杉+糙皮桦-大齿槭+尾萼蔷薇-高原露珠草+星果草群系发育较好,高大树木占有较大的比例,是神农架川金丝猴最适宜栖息地.7个植被型物种丰富度指数在群落梯度上呈规律性波动.其中针叶林和针叶-阔叶混交林中,物种丰富度指数在群落梯度上的总体趋势表现为灌木层＞草木层＞乔木层;在常绿阔叶林和常绿-落叶阔叶混交林中,该趋势为灌木层＞乔木层＞草本层;在落叶阔叶林中,其丰富度指数的趋势为灌木层＞草本层和乔木层.不同植被类型川金丝猴食源植物种类在群落梯度上的变化趋势与物种丰富度指数相同,但地衣类植物作为川金丝猴冬季的重要食物只在针叶林和针叶-阔叶混交林中生长.本研究为制定栖息地保护计划,更好地保护神农架川金丝猴提供了科学理论依据.